It's cutting it very tight, and I don't know if IB will check through on two separate tickets, but you should assume they won't. You know, I'll guess, the danger of separate tickets is that, if you don't make the IB Express flight for whatever reason (for example, the JFK flight is delayed by an hour, which would not be unusual), the return portion of that flight will also be cancelled. IB has no obligation to accommodate you; they might, but the probably won't.